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On Modelling Minimal Disease Activity.

ABSTRACT: To explore methods for statistical modelling of minimal disease activity (MDA) based on data from intermittent clinic visits.The analysis was based on a 2-state model. Comparisons were made between analyses based on "complete case" data from visits at which MDA status was known, and the use of hidden model methodology that incorporated information from visits at which only some MDA defining criteria could be established. Analyses were based on an observational psoriatic arthritis cohort.With data from 856 patients and 7,024 clinic visits, analysis was based on virtually all visits, although only 62.6% provided enough information to determine MDA status. Estimated mean times for an episode of MDA varied from 4.18 years to 3.10 years, with smaller estimates derived from the hidden 2-state model analysis. Over a 10-year period, the estimated expected times spent in MDA episodes of longer than 1 year was 3.90 to 4.22, and the probability of having such an MDA episode was estimated to be 0.85 to 0.91, with longer times and greater probabilities seen with the hidden 2-state model analysis.A 2-state model provides a useful framework for the analysis of MDA. Use of data from visits at which MDA status can not be determined provide more precision, and notable differences are seen in estimated quantities related to MDA episodes based on complete case and hidden 2-state model analyses. The possibility of bias, as well as loss of precision, should be recognized when complete case analyses are used.

SUBMITTER: Jackson CH

PROVIDER: S-EPMC4949508 | biostudies-literature | 2016 Mar

REPOSITORIES: biostudies-literature

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On Modelling Minimal Disease Activity.

Jackson Christopher H CH Su Li L Gladman Dafna D DD Farewell Vernon T VT

Arthritis care & research 20160301 3

<h4>Objective</h4>To explore methods for statistical modelling of minimal disease activity (MDA) based on data from intermittent clinic visits.<h4>Methods</h4>The analysis was based on a 2-state model. Comparisons were made between analyses based on "complete case" data from visits at which MDA status was known, and the use of hidden model methodology that incorporated information from visits at which only some MDA defining criteria could be established. Analyses were based on an observational p ...[more]

PMID: 26315478

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Project description:OBJECTIVE:We aimed to standardize the definition of low disease activity in rheumatoid arthritis (RA) using the Outcome Measures in Rheumatology (OMERACT) group's proposed definition of minimal disease activity. METHOD:Based on a nationwide RA database, we proposed new Boolean low disease activity criteria using OMERACT's core set definition of minimal disease activity that requires the fulfillment of at least five of the following seven core set measures: a pain score of 2 or less, a swollen joint count (SJC28) of 1 or fewer, a tender joint count of 1 or fewer, a Health Assessment Questionnaire score of 0.5 or less, a Physician's Global Assessment score of 1.5 or less, a Patient's Global Assessment score of 2 or less, and an erythrocyte sedimentation rate (ESR) of 20 mm/h or less. Using receiver operating characteristic analysis, we determined the cutoffs for the Simplified Disease Activity Index (SDAI), Clinical Disease Activity Index (CDAI), Routine Assessment of Patient Index Data 3 (RAPID3), and the Disease Activity Score in 28 joints (DAS28)-ESR. RESULTS:Of 8298 patients, 56.2% met the proposed Boolean low disease activity criteria. We determined an SDAI score of 5.5 or less and a CDAI score of 5 or less to be the new cutoffs, and we chose a DAS28 of 2.85 or less (the original cutoff for DAS-based minimal disease activity) and a RAPID3 score of 6 or less (the original cutoff for RAPID3-based low disease activity) with or without a swollen joint count (SJC) (SJC of 2 or fewer) as the cutoffs for DAS28 and RAPID3. The agreement between the new cutoffs for DAS28 of 2.85 or less vs. CDAI score of 5 or less, CDAI score of 5 or less vs. RAPID3 score of 6 or less (with SJC of 2 or fewer), and DAS28 of 2.85 or less vs. RAPID3 score of 6 or less (with SJC of 2 or fewer), was 0.619, 0.612 (0.702), and 0.474 (0.531), respectively. CONCLUSION:OMERACT's minimal disease activity definition may be used to standardize the criteria for low disease activity.

Project description:Nuclear factor-kappa B (NF-κB) is a ubiquitous transcription factor that regulates immune and cell-survival signaling pathways. NF-κB has been reported to be present in neurons wherein it reportedly responds to immune and toxic stimuli, glutamate, and synaptic activity. However, because the brain contains many cell types, assays specifically measuring neuronal NF-κB activity are difficult to perform and interpret. To address this, we compared NF-κB activity in cultures of primary neocortical neurons, mixed brain cells, and liver cells, employing Western blot of NF-κB subunits, electrophoretic mobility shift assay (EMSA) of nuclear κB DNA binding, reporter assay of κB DNA binding, immunofluorescence of the NF-κB subunit protein p65, quantitative real-time polymerase chain reaction (PCR) of NF-κB-regulated gene expression, and enzyme-linked immunosorbent assay (ELISA) of produced proteins. Assay of p65 showed its constitutive presence in cytoplasm and nucleus of neurons at levels significantly lower than in mixed brain or liver cells. EMSA and reporter assays showed that constitutive NF-κB activity was nearly absent in neurons. Induced activity was minimal--many fold lower than in other cell types, as measured by phosphorylation and degradation of the inhibitor IκBα, nuclear accumulation of p65, binding to κB DNA consensus sites, NF-κB reporting, or induction of NF-κB-responsive genes. The most efficacious activating stimuli for neurons were the pro-inflammatory cytokines tumor necrosis factor α (TNFα) and interleukin-beta (IL-β). Neuronal NF-κB was not responsive to glutamate in most assays, and it was also unresponsive to hydrogen peroxide, lipopolysaccharide, norepinephrine, ATP, phorbol ester, and nerve growth factor. The chemokine gene transcripts CCL2, CXCL1, and CXCL10 were strongly induced via NF-κB activation by TNFα in neurons, but many candidate responsive genes were not, including the neuroprotective genes SOD2 and Bcl-xL. Importantly, the level of induced neuronal NF-κB activity in response to TNFα or any other stimulus was lower than the level of constitutive activity in non-neuronal cells, calling into question the functional significance of neuronal NF-κB activity.

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Project description:BACKGROUND/OBJECTIVES:A cascade of gene activations under the control of Notch signalling is required during T-cell specification, when T-cell precursors gradually lose the potential to undertake other fates and become fully committed to the T-cell lineage. We elucidate how the gene/protein dynamics for a core transcriptional module governs this important process by computational means. METHODS:We first assembled existing knowledge about transcription factors known to be important for T-cell specification to form a minimal core module consisting of TCF-1, GATA-3, BCL11B, and PU.1 aiming at dynamical modeling. Model architecture was based on published experimental measurements of the effects on each factor when each of the others is perturbed. While several studies provided gene expression measurements at different stages of T-cell development, pure time series are not available, thus precluding a straightforward study of the dynamical interactions among these genes. We therefore translate stage dependent data into time series. A feed-forward motif with multiple positive feed-backs can account for the observed delay between BCL11B versus TCF-1 and GATA-3 activation by Notch signalling. With a novel computational approach, all 32 possible interactions among Notch signalling, TCF-1, and GATA-3 are explored by translating combinatorial logic expressions into differential equations for BCL11B production rate. RESULTS:Our analysis reveals that only 3 of 32 possible configurations, where GATA-3 works as a dimer, are able to explain not only the time delay, but very importantly, also give rise to irreversibility. The winning models explain the data within the 95% confidence region and are consistent with regard to decay rates. CONCLUSIONS:This first generation model for early T-cell specification has relatively few players. Yet it explains the gradual transition into a committed state with no return. Encoding logics in a rate equation setting allows determination of binding properties beyond what is possible in a Boolean network.

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On Modelling Minimal Disease Activity.

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On Modelling Minimal Disease Activity.

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